Microbial community dynamics in a traditional Swiss mountain cheese over 142 years of cheesemaking

The history of cheesemaking is deeply intertwined with the evolution of microbial communities, from spontaneous fermentation to modern, standardized practices. The rapid technological changes of the last century likely induced profound alterations in cheese microbial communities, yet this remains largely underexplored. Using shotgun metagenomics and 16S rRNA amplicon sequencing, we examined microbial community changes in Raclette du Valais, a traditional Swiss cheese, using preserved wheels from 1875 to 2017 from the same Alpine dairy. Our results reveal that significant differences in microbial community composition coincide with changes in production practices. The oldest cheese harbored a distinct bacterial community, dominated by Lactiplantibacillus paraplantarum, Streptococcus thermophilus, Pseudolactococcus laudensis, and gut-associated taxa. Antibiotic-resistance genes mirrored historical antibiotic use, lactic acid bacteria domestication predated the studied period, and bacteriophage genera from 1875 were already comparable to those of modern cheese factories. These findings highlight how human practices have shaped cheese microbiomes over time.